Most third party sellers aren't permitted to set shipping fees. I think the only difference is the contracted selling partners. The fees Amazon charges seem to be arbitrary as well, sometimes the seller takes a hit on shipping fees, sometimes they are covered. However I don't think Amazon offers combined seller shipping for their third party sellers.
Amazon doesn't offer/promote combined shipping for 3rd party sellers although you can always send a message to the seller asking them if they would be willing to do so. I have tried this twice and the first time was successful while the second time the seller told me it was against Amazon policy. I actually called Amazon to research this and was told that it is at the seller's discretion.
You may find it difficult to locate a seller who is willing to do it though, because of Amazon's arbitrary seller performance guidelines. Too many refunds (regardless of the reason) can negatively impact the 3rd party's seller account.
EDIT: To clarify, the only way most 3rd party sellers can give you a combined shipping discount is to refund part of your purchase price since the shipping rate is already set through Amazon. The "featured merchants" who are able to set shipping rates on their own may be able to make an adjustment prior to your purchase.
>>> the second time the seller told me it was against Amazon policy. I actually called Amazon to research this and was told that it is at the seller's discretion. <<<
Here's the problem: Amazon collected the full price of shipping, but takes a cut before sending some of that money to the seller. The seller only has part of the shipping fees to give back even if they wanted to.
With books and media that can be sent Media Mail, they may be able to cut you a deal, and give you a partial refund without losing money. But for non-media items, what they get from Amazon often doesn't even cover their costs, even if they combine the items into one shipment.
Also, USPS, UPS and FedEx all have started using dimentional weight for large, but light packages in the last couple years, so combining two larger items might cost more than shipping them both seperately.
While Amazon, with their low COGS, can absorb part of the cost of shipping into their prices, 3rd party sellers are usually working with such a small margin that asking them to give a price break for combined shipping is a hard pill to swallow for them, especially the smallest of them.